{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:28Z","timestamp":1772138068949,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T00:00:00Z","timestamp":1718582400000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006975","name":"Indiana Clinical and Translational Sciences Institute funded","doi-asserted-by":"crossref","award":["UL1TR002529"],"award-info":[{"award-number":["UL1TR002529"]}],"id":[{"id":"10.13039\/100006975","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https:\/\/github.com\/nianqiaoju\/snp-slice.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae344","type":"journal-article","created":{"date-parts":[[2024,6,14]],"date-time":"2024-06-14T18:48:44Z","timestamp":1718390924000},"source":"Crossref","is-referenced-by-count":5,"title":["SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to 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